She has been remanded in custody until 15 February, police documents show.
The charges include breaching import and export laws, and possession of unlawful communication devices.
Her whereabouts are still unclear, but it has been reported that she is being held at her residence in the capital, Nay Pyi Taw.
Deposed President Win Myint has also been charged, the documents show - in his case with violating rules banning gatherings during the Covid pandemic. He has also been remanded in custody for two weeks.
Neither the president nor Ms Suu Kyi have been heard from since the military seized power in the early hours of 1 February.
The coup, led by armed forces chief Min Aung Hlaing, has seen the installation of an 11-member junta which is ruling under a year-long state of emergency.
The military sought to justify its action by alleging fraud in last November's elections, which Ms Suu Kyi's National League for Democracy (NLD) won decisively.